Microbiology – Rapid Review

Just a bunch of notes here….

Acid-fast cell walls

From wiki: Acid-fast organisms are difficult to characterize using standard microbiological techniques (e.g. Gram stain – if an acid-fast bacillus (AFB) was gram stained, the result would be an abnormal gram positive organism, which would indicate that further testing was necessary), though they can be stained using concentrated dyes, particularly when the staining process is combined with heat. Once stained, these organisms resist the dilute acid and/or ethanol-based de-colorization procedures common in many staining protocols, hence the name acid-fast.[2]

Waxy lipid (mycolic acid) bound to peptidoglycan


Resting cells
Resistant to desiccation, heat, chemicals
Bacillus, Clostridium

streptococcus aureus (toxin mediated)

Young woman,102 degree fever two days after menses, uses tampons. After several days the fever, dizziness, hypotension, myalgias, diffuse rash on the chest, Toxin is TSST-1, desquamation of the palms,
Catalase positive, Coagulase positive.

Staphylococcus epidermidis

Ten days after chemotherapy for non-Hodgkin’s lymphoma, a middle aged man, fever, erythema and tenderness at the insertion site of the IV catheter. Blood cultures positive, original catheter removed, patient is started on antibiotics, Catalase positive and Coagulase negative.

Streptoccocus pyogenes

A young child, fever, skin rash localized around the lips and face. The rash is pustular with yellow crusts. Cultures shoe bacteria show Gram positive cocci in chains that are Beta-hemolytic.

Staphlococcus aureus (infectious)
IV-drug user, high fever, signs of heart failure, notable heart murmur, echocardiogram reveals tricuspid valve vegetations, patient is immediately begun on IV antibiotics.

Helicobacter pylori

A 65 year old male, upper abdominal pains which become worse after meal. Knowing the patient’s history, doctor is about to prescribe an H2 blocker but biopsy of stomach mucosa and urease breath test performed, doctor to prescribe antibiotics.

H. pylori
Blood type O, peptic ulcers (duodenal or gastric ulcers), bacteria produce ammonia (via urease) to protect from gastric acid.

Yersinia pestis

Traveler, Mexico presents to the ER with fever, dark black skin patches, enlarged, painful lymph nodes in groin. Doctors begin treatment immediately and inquire about possible flea bites.

Vibrio cholerae

Female church missionary visiting India, ER, severe dehydration, thirsty, decreased skin turgor, tachycardia, abrupt diarrhea this morning and complains of large amount of watery volumes she is excreting. No fever, doctor treats with fluids and electrolytes.

Vibrio cholerae
Turns yellow on TCBS agar, comma shaped gram neg. rods, rice-water diarrhea, carried in FOOD, WATER, SHELLFISH

Mycoplasma pneumoniae

Young woman on an army base complains of cold, malaise, chills, sore throat, and dry cough. Chest radiograph interstitial infiltrate. Labs – serum was capable of agglutinating erythrocytes when incubated at 4 degrees C, doctor prescribes erythromycin.

Mycoplasma pneumoniae
Atypical pneumonia (walking pneumonia), no invasion, fried-egg appearance, erythromycin, only bacteria to have no cell wall AND cholesterol in membranes, prisons, military bases

Clostridium perfringes
Man, New York City ER, stabbed 2 days ago. Muscles in arm hurt and on palpation small air bubbles are felt below skin and generates a crackling sound when touched

Clostridium perfringens

gas gangrene, spores in soil, deep laceration, ALPHA TOXIN, anaerobic, gram pos. rod, non motile, hyperbaric oxygen to kill

Escherichia coli
A series of patients, small town, bloody diarrhea, fatigue, and confusion. All same fast-food burger restaurant
Escherichia coli
enteritis, UTI, Uremic syndrome (HUS), normal flora, ETEC, EPEC, EAEC, EHEC, EIEC, Gram neg. rod, ferments lactose on MaConkey AGAR, EHEC (0157:H7), LT TOXIN, AB2 TOXIN, raise cAMP, ST – raise cGMP, gram neg. sepsis, NEONATAL MENINGITIS

Salmonella typhi
Woman, recently returned international trip complains, abdominal pain, high fever, headache and constipation.
Physical exam reveals rose spots (faint pink macules) as well as hepatosplenomegaly.
Stool sample reveals motile bacteria, does not ferment lactose.

Clostridium difficile
An elderly woman comes to the doctor with a fever and loose bowels from what she thinks is from taking clindamycin a couple of weeks ago from an infection.
Sigmoidoscopy of her colon reveals yellow-white plaques which the doctor predicted after analyzing her stools for toxins which revealed Toxin B.

Double-stranded DNA, enveloped viruses
Simplexvirus (HHV-1 and HHV-2)
Varicellovirus (HHV-3)
Cytomegalovirus (HHV-5)
Roseolovirus (HHV-6)
Kaposi’s sarcoma (HHV-8)
Some herpes viruses can remain latent in host cells

Single-stranded RNA, + strand, nonenveloped
Poliovirus and coxsackievirus
Hepatitis A virus

Single-stranded RNA, + strand, enveloped
Upper respiratory infections


Single-stranded RNA, – strand, multiple RNA strands
Envelope spikes can agglutinate RBCs
Influenzavirus (influenza viruses A and B)
Influenza C virus

Single-stranded RNA, 2 RNA strands, produce DNA
Use reverse transcriptase to produce DNA from viral genome
Lentivirus (HIV)
Oncogenic viruses
Includes all RNA tumor viruses

Picornaviridae Rhinovirus
A woman presents with a runny nose, sneezing and a sore throat. She suffers similar symptoms every year often at the same time as other members of her family. Her symptoms go away within a week, except for nasal discharge that persists for a few more days. What RNA virus below do you think she has?

Herpesviridae Varicellovirus
Varicella-Zoster (VZV) or Herpesvirus 3
An 82-year old woman complains to her doctor of a burning, painful rash on her chest. A physical exam reveals fever and a vesicular, erythematous rash limited to the right side of her chest. The physician confirms a diagnosis by a Tzanck smear of the lesions. The physician gives acyclovir and explains that the rash will get better but the pain may persist longer

Herpesviridae Simplexvirus, HSV-2
or Herpesvirus 2
At a preterm evaluation a 31 year old pregnant mom reports pain on urination and a burning, itching sensation in the genital area. An exam reveals a vesicular rash where a Tzanck smear is performed The mom is given acyclovir and is informed that should the infection persist her child will have to be delivered by cesarean section.

Retroviridau Lentivirus,
HIV-1, HIV-2 (West Africa)
50 year old homeless man complains to the ER doctor of fever and cough which has lingered for several weeks. This is accompanied by weight loss. Sputum reveals presence of the fungal infection Pneumocystis jirovecii. What do you immediately suspect? Rhinovirus, Coxsackievirus B, HIV or Coronavirus?

Candida albicans
Patient presents at the free clinic complaining of painful swallowing and severe chest pains. Several months ago the patient said they had a white membrane covering the tongue. What do you suspect?

Trichophyton (Ringworm -TINEA infections)
A high school football player presents to the local clinic with itchiness between his toes and inguinal area. Skin scrapings from the patients feet reveal branched hyphae

Tinea capitis
scalp, eyebrows and eyelashes,
Microsporum and Trichophyton



Tinea corporis
smooth or glabrous skin, any dermatophyte

Tinea cruris
Trichophyton and Epidermophytom, groin

Tinea pedis
Trichophyton and Epidermophytom, foot

Tinea unguium
Trichophyton, nails

Blastomyces dermatitidis, Blastomycosis

A man from Missouri develops weakness and night sweats. His physician notices sores on the patient’s skin. Biopsy of the skin lesions reveals large budding yeast with broad bases. . The doctor starts the man immediately on amphotericin B.

Plasmodium falciparum, vivax, ovale, malariae, Malaria
Patient with chills, extreme fever and debilitating fatigue goes to the local physician. Physical exam reveals yellow sclera and splenomegaly. CBC reveals low hematocrit and urinalysis reveals hemoglobinuria. The doctor finds out the patient had been doing international travels to Africa and India. A blood smear shows ring shapes.

Entamoeba histolytica
After a camping trip to Mexico, a patient visits her doctor complaining of loose stools and abdominal cramps. The patient describes the stools as having flecks of blood and lots of mucus. The doctor starts the patient on metronidazole and orders a CT scan to detect any liver abscesses.

Toxoplasma gondii

An AIDS patient is brought to the ER after suffering a grand mal seizure. The patient informs the ER physician that he has been also suffering persistent headaches in the past few weeks. Knowing opportunistic diseases affect AIDS patients what are you thinking?

Giardia lamblia

A student cuts short a backpacking trip to Yosemite Park after developing diarrhea that he reports is nonbloody but smelly very bad. On further questioning, the student tells his doctor that he has been drinking water from a fresh water spring. Diarrhea sample reveals 2-nuclei motile amoeba with a tear-drop shape and 4 pairs of flagella.

Schistosoma species, Schistomiasis, Blood Fluke, Katayama Fever
An African woman visits her doctor after urinating blood. In her history, she states that she worked in freshwater rice fields before coming to the U.S. Cytoscopic examination of the bladder shows inflammatory lesions and urinalysis demonstrates eggs. She is started on praziquantel

Enterobius vermicularis
A teacher reports to a parent that her child has been scratching his anal region. The doctor recommends a “Scotch tape” test based on past cases with similar complaints.

Ascaris lumbricoides
A man in Louisiana develops coughing, fever and abdominal pain. His doctor orders a series of X-rays that show pulmonary infiltrates characteristic of pneumonia, as well as intestinal images consistent with obstruction. On CBC the patient has increased eosinophils

Shigella dysenteriae
Child in daycare, very watery diarrhea with blood, mucous in stool as well as cramps, fever, bacteria is a non lactose fermenter.

Shigella dysenteriae

non-lactose fermenter, blood watery diarrhea with mucous

Streptococcus pneumoniae
local – lobar pneumonia, ottis media, Systemic – meningitis, gram pos. cocci, catalase neg. a-hemolytic

Y. enterocolitica
pseudo appendicitis, enterocolitis (bloody diarrhea), mesenteric adentis, ENTEROTOXIN, invades and causes inflammation, replicates in nodes, manifests differently with ages

Flat yellow colonies on TCBS, AB5 toxin, type O
What kind of agar does Vibrio cholera grow on?
What type of toxin? What blood group more susceptible?

Blood to organ systems – and brain, Rabies goes through nerves to CNS
Pharyngitis, impetigo, erysipelas, cellulitis, gram ps. cocci, catalase negative Streptococcus pyrogenes
Lyme disease travels through the body how? How about Rabies?

Streptococcus parasanguis, S. mutans

Staphylococcus aureas
S. epidermidis

Streptococcus pneumoniae
Neisseria meningitidis

Various streptococci

organisms commonly associated with infections of the sinuses
S. pneumoniae, S. aureus, H. influenzae, and Moraxella catarrhalis


Streptococci- normal in upper respiratory tract, but, if they get into blood stream can cause this…

Exotoxins produced by
gram positive bacteria

Endotoxins produced by
gram negative bacteria, e.g., Lipid A

Streptococci pyogenes
Gram positive cocci
Catalase negative
Transient colonization in upper respiratory tract and skin,
Adherence is mediated using lipoteichioic acid and F-& M- proteins

Evading the immune response:
Capsule – interferes with

Gram resistant organisims
Intracellular Bacteria


(coagulase +)- S. aureus
(coagulase -) – S. epidermidis
and S. saprophyticus
Gram + cocci
Catalase +
Catalase converts H202 to H20 and 02
Coagulase converts fibrinogen to fibrin

Coagulase-negative ??? are part of skin normal flora

Polysaccharide capsule
Role in preventing phagocytosis
Slime layer
Varies among species; role in adhesion
Protein A
Binds Fc receptors of immunoglobulin IgG
Exotoxins (e.g., superantigen family)

Staphylococcal infection
scalded skin syndrome, food poisoning, and toxic shock syndrome

Coagulase-negative Staphylococci
Considered less virulent than S. aureus
Most commonly encountered in association with prosthetic devices
Pathogenesis is associated with the slime layer and biofilm

Staphylococci: Diagnostics
Sheep blood agar
beta-hemolysis, Mannitol-salt agar
Mannitol-salt agar: useful selective and differential media because most other bacteria that are commensals on skin are inhibited by the 7.5% NaCl

Mannitol-salt agar
contains the sugar mannitol and the pH indicator phenol red.
If an organism can ferment mannitol, an acidic byproduct is formed that will cause the phenol red in the agar to turn yellow.

All staphylococci are catalase ?

? is the primary test used to distinguish S.aureus from other staphylococcal species

Staphylococci are catalase ?, whereas streptococci are catalase ?
positive, negative

Gram positive cocci; tendency to grow in chains
Nonmotile, non-spore forming

Streptococcus pyogenes
Group A Streptococcus (GAS)
Colonization: pharynx, nares
 Transmission: respiratory droplets; sneezing, coughing
Virulence Factors:
Hyaluronic capsule
C5a peptidase
M-protein-Major virulence factor
Extends through cell wall from cell membrane
Hemolysins: responsible for lysing erythrocytes
Pyrogenic exotoxins – Spe (A, B, C, F)

Pharyngitis caused by S. pyogenes
Reddened pharynx with exudates generally present
Most common of streptococcal infections
Generally self-limiting
Most common in children, especially ages 5-15

S. pyogenes
? adheres via Protein F and lipoteichoic acid
Possibly internalize into oropharyngeal epithelial cells
Inflammatory response

Streptococcus pneumoniae
Oval or lancer shaped, diplococci
Virulence factors-
**polysaccharide capsule protects bacterium from phagocytosis, Utilize secretory IgA protease to prevent the interaction of IgA and mucin to trap and clear bacteria, Pneumolysin, a cytotoxin, binds cholesterol in the host cell membrane and creates pores to destroy both ciliated epithelial cells and phagocytes

Streptococcus pneumoniae

Typical and lobar pneumonia
Blood-tinged “rusty” sputum
Sinusitis and Otitis Media

Streptococcus pneumoniae
Patient is a 65-year old male who complains of sudden onset of fever, chills, chest pain (pleuritis) and cough. His sputum is brown/rusty.

Streptococcus pneumoniae
Gram stain
Culture: enriched media supplemented with blood products
Lacks catalase
Susceptibility to optochin, Optochin test
-disk diffusion method

MacConkey Agar
Lactose Fermentation
Pink- Lactose fermenter
Clear- Non-lactose fermenter

Escherichia coli
Gram negative rods
Facultative anaerobic
Lactose fermenter
Most common gram-negative rods in the gastrointestinal tract
Most infections are endogenous although strains causing gastroenteritis are generally acquired exogenously

Escherichia coli
Urinary Tract Infection: MOST COMMON
Fecal/colon contaminate urethra
Adhesion: P pili (pyelonephritis-associated pili)
bind to cells lining the bladder and upper urinary tract
Neonatal meningitis
K1 capsule

Enterohemorrhagic E. coli (EHEC):
Mostly associated with eating undercooked beef, unpasturized fruit juices (O157:H7), Mild diarrhea to Hemorrhagic colitis (bloody diarrhea); can develop into hemolytic uremic syndrome, Pili, Shiga toxin 1 & 2
No invasion,
Hemolytic uremic syndrome- associated with renal failure

Salmonella, S. typhi
Non-typhoid (S. enteritis, S. typhimurium)

Gram negative rods
S. typhi
Motile, Non-lactose fermenting, Produces H2S, Sensitive to acid
Virulence factors:Secreted invasion proteins (SSpS), LPS, Capsule

S. Typhi- can survive in gall bladder of humans- carriers
Fecal-oral route
S. Enteritidis, S. typhimurium- on reptiles, domestic animals
Contaminated poultry, eggs, dairy products

Typhoid fever

Infection begins in ileocecal region
Invade M-cells in Peyers patches and enterocytes
Replicate in endocyctic vacuoles
Resistant to macrophage killing
Proteins interfere with fusion of lysosome-phagosome
Travel through blood to spleen, liver, septicemia
Infect biliary system (Gall bladder, liver)

Typhoid fever
5 to 21 days incubation period
Patients present with abdominal pain, fever, chills
Rose spots can develop: a rash consisting of faint pink macules on the trunk and abdomen.
Hepatosplenomegaly, intestinal bleeding and/or perforation caused by erosions of Peyer’s patches

Gram negative rods
Non-lactose fermenters
Nonmotile, Humans are the only reservoir, Transmitted by fecal-oral spread, Contaminated hands
SHIGA toxin

S. dysenteriae
Causes enterocolitis/ shigellosis
Bloody diarrhea
Fever, abdominal pain
Stool culture
Does not ferment lactose
Does not produce H2S
Hektoen-enteric agar production of H2S, which makes colonies light green with black centers.

Yersinia pestis
Transmission via rodents fleas
Gram-negative rods
Non-lactose fermenter,
Human-to-human transmission when there is pulmonary involvement

Yersinia enterocolitica
Consumption of contaminated meat, milk, or water, pet feces (e.g., puppies)
Gram-negative rods,
Non-lactose fermenter

Yersinia enterocolitica

Can grow in cold temperatures
Motile (25C), nonmotile (37C)
Clinical Diseases
Incubation period 1-10 days
Diarrhea, fever, abdominal pain
Pseudoappendicitis common in children
Manifestations in adults can include arthritis and septicemia

Facultative anaerobe
Polar flagella, motile
Curved rods
Grow naturally in estuarine and marine environments worldwide
able to survive and replicate in contaminated waters with increased salinity.
association between pathogenic ? infections and the consumption of shellfish

Growth on alkaline media
Vibrio require salt for growth.
TCBS, thiosulfate citrate bile salt sucrose medium
Susceptible to stomach acids.

Vibrio Cholerae

Spread by contaminated water and food
Fecal-oral spread
Virulence factors:
Binding site for lysogenic bacteriophage that encodes genes for cholera toxin and other virulence factors
mediates adherence to intestinal mucosal cells
Cholera toxin
complex A-B toxin that is structurally and functionally similar to the heat-labile enterotoxin of Escherichia coli
Vibrio Cholerae
Abrupt onset of watery diarrhea and vomiting about 2 to 3 days after ingestion of the bacteria
“rice-water” stools
feces-streaked stool specimens become colorless and odorless, free of protein, and speckled with mucus
The resulting severe fluid and electrolyte loss can lead to dehydration

Helicobacter pylori
Gram-negative spiral rods
Polar flagella
Survives in a thick and viscous mucus layer the overlays the gastric mucosa (maintains pH ~7.4)
Urease- produces ammonia that neutralizes gastric acids, allowing survival in stomach acid
Motility- migrate to the most favorable pH gradient and adhere to the gastric epithelial cells by multiple surface-adhesion proteins

Helicobacter pylori
Urease byproducts
Mucinase- aids in the penetration of mucous layer
Vacuolating cytotoxin A (VacA)-
Toxin is activated by acid of the stomach
produces vacuoles in epithelial cells after being endocytoses

Borrelia burgdorferi
White-footed mice
White-tailed deer
Transmitted by Ixodes ticks
Ixodes scapularis in Northwest (e.g., Connecticut), Midwest (e.g., Wisconsin)
Ixodes pacificus on West Coast
Incidence of disease in late spring/ early summer

Borrelia burgdorferi: Lyme Disease

weeks to months after stage 1
Smaller skin lesions
Aseptic meningitis
Bells palsy (cranial nerve palsies)
cardiac, joint and muscle pain

Gram positive rods
Spore forming
Ubiquitous (e.g., soil)

Clostridium perfringens
Large, boxcar shaped
Virulence factors:
Alpha toxin
Phospholipase C
Lyses erythrocytes, platelets,
 leukocytes and endothelial cells
Increases vascular permeability

Clostridium perfringens
Gas Gangrene/Cellulitis/ wound infection
Tissue necrosis involving muscle, gas production
Crepitus- cracking consistency to the skin b/c of gas
Destruction of muscle tissue
Can be fatal unless treated
Diarrheal illness
Watery diarrhea to a more severe necrotizing enterocolitis

Clostridium tetani

Small rods with tennis racquet shape due to the presence of terminal sport
Transmitted via puncture wounds/ trauma
Rusty nail
Virulence factors

Carried intra-axonal via retrograde transport to CNS
Toxin also spreads hematogenously
Blocks release of inhibitory mediators (eg., GABA & glycine) at spinal synapses
Excitatory neurons are unopposed= extreme muscle spasms

Clostridium botulinum
Found in the soil and dust
Transmission is foodborne or traumatic implantation
C. botulinum toxin
Absorbed by the gut and carried to peripheral nerves
Blocks release of acetylcholine= blocking neurotransmission at peripheral cholinergic synapses
Flaccid paralysis

Clostridium difficile
In some individuals- part of normal flora, GI tract
Endogenous or exogenous transmission
Antibiotic resistance
Enterotoxin-toxin A
Causes diarrhea


Smallest free-living extracellular bacteria
Capable of passing through a 0.45-µm filter, which retains most other bacteria
Do not have a cell wall (missing peptidoglycan)
Not seen on gram stain
Obligate aerobe

Mycoplasma pneumoniae
Virulence factors
P1 adhesin
Adherence to respiratory epithelium
Inhibits ciliary action
Cilia and ciliated epithelial cells are destroyed; causes sloughing of cells

Mycoplasma pneumoniae
Primary atypical “Walking” pneumonia
Low-grade fever, headache, dry-hacking nonproductive cough, myalgia, Tracheobronchitis
Inflammation of the bronchi marked by nonproductive cough, fever, sore throat
 Diagnosis: eaton agar Production of cold agglutinins

a complete virus particle that consists of one or more molecules of DNA or RNA enclosed in a protein shell (capsid) and, in some cases, a lipid envelope

The ? is a rigid structure able to withstand harsh environmental conditions (particularly important for naked viruses)

The ? is a membrane composed of lipids, proteins, and glycoproteins. The membranous structure of the envelope can be maintained only in aqueous solutions. It is readily disrupted by drying, acidic conditions, and detergents, which results in inactivation of the virus.

All of the negative-strand RNA viruses are enveloped/naked?


Genome of ? differ from other ssRNA viruses in that their positive-stranded RNA genomes are converted to DNA rather than serving as mRNA.
 dsDNA copy of the ssRNA genome.

Most ? viruses enter the cell by receptor-mediated endocytosis or by direct penetration

? viruses fuse their membranes with cellular membranes to deliver the nucleocapsid or genome directly into the cytoplasm; they can also enter the cell by receptor-mediated endocytosis

Reverse Transcriptase- enzyme which can convert RNA into DNA

Nuclear DNA replication


Cytoplasmic DNA replication


Latent in the trigeminal and dorsal root ganglia. On reactivation, the virus replicates and is released along the entire neural pathway to infect the skin, causing a vesicular rash along the entire dermatome, known as herpes zoster, or shingles.

Pain and vesicles restricted to one dermatome
Fifth and sixth decade of life
Reactivation of latent infection

VZV: Diagnosis

Cytopathologic effects (CPEs) can be identified in a Tzanck smear

Scrapings from base of vesicles
CPEs include syncytia, and Cowdry type A intranuclear inclusions

Herpes Simplex Virus (HSV) 1 & 2
The two types, Target cells: Mucoepithelial cells, Latency: neurons & ganglia
First type: (trigeminal ganglia), second type: (sacral ganglia) contact & sexually transmitted
transmitted in vesicle fluid, saliva, and vaginal secretions

Approximately 85% of genital herpes are caused by

HSV 1 & 2: Diagnosis & Treatment
Tzanck smears of scrapings from a vesicle’s base-Cowdry type A, intranulcear inclusions, syncytia
Giemsa, Wright stain
Immunoflourescence of tissue sample or vesicle fluid for viral particles
Viral cultures
Virus can be obtained from vesicles

Enteroviruses, Rhinoviruses, Hepatitis A
Positive-sense (+), single-stranded (ss) RNA viruses

Positive-sense (+), single-stranded (ss) RNA viruses, SARS

Small, naked, icosahedral
Virus replicates in cytoplasm
Most picornaviruses inhibit cellular RNA and protein synthesis during infection,
Two genera

Small, nonenveloped single-stranded (+) RNA viruses
Of Medical Importance
Coxsackievirus A and B
Fecal-oral transmission;
Capsids are very resistant
Asymptomatic shedding

Enters through GI
Replicates in pharynx, gut, submucosal lymphoid tissue
Viremia spreads the virus to receptor-bearing target tissues
Immune response usually contains viral infection
Antibody is the major protective immune response to the enteroviruses

Enters through GI tract
ssRNA (+)
Immunity is lifelong


Virus can enter the CNS directly from the blood or axonal transport in nerves
Cytolytic for motor neurons of the anterior horn and brain stem
Destruction of neurons is accompanied by inflammatory infiltrate and polymorphonuclear leukocytes, lymphocytes, and macrophages

Coxsackievirus A & B
Nonenveloped, ss(+) RNA
They are divided into two groups, A and B, on the basis of certain biologic and antigenic differences

Coxsackievirus A
Fever, sore throat, pain on swallowing, anorexia, and vomiting
The classic finding is vesicular ulcerated lesions around the soft palate and uvula, HAND-FOOT-and-MOUTH disease
vesicular exanthem
Rash, vesicular lesions on the hands, feet, mouth, and tongue
Most common in children

Coxsackievirus B
Abrupt onset of spasmodic pain in chest or upper abdomen commonly associated with fever, malaise, and headaches, the striated muscle is the actual anatomic structure targeted; the striated intercostal muscles necrose.
Myocardial and pericardial infections: The destruction and damage to the heart cells results in myocarditis and heart failure
Cyanosis, tachycardia, cardiomegaly, and hepatomegaly occur. 

Small, nonenveloped
Ss (+) RNA
Icosahedral capsid
Over 100 serotypes; makes vaccine development difficult
Not stable under acidic conditions
Growth at 33C (temp of nose and large airway)
Peak summer and fall
Spread via contaminated respiratory secretion, on fomites (e.g., by hands or on contaminated inanimate objects).

The virus enters through the nose, mouth, or eyes and initiates infection of the upper respiratory tract, including the throat
Viral replication takes place primarily in nonciliated lymphoepithelial cells of the nasopharynx.
Infection of lower airways can occur; more common in children

Most important cause of the common cold and upper respiratory tract infections
Can cause otitis media and sinusitis
May exacerbate asthma, Usually begins with sneezing, followed by rhinorrhea (runny nose), which may lead to symptoms of nasal obstruction, Mild sore throat also occurs, along with headache and malaise but usually without fever. The illness peaks in 3 to 4 days, but the cough and nasal symptoms may persist for 7 to 10 days or longer.

Enveloped, positive (+) RNA genome.
The glycoproteins appear as club-shaped projections that appear as a halo (corona) around the virus. 

Infect epithelial cells.
Infection remains localized to the upper respiratory tract because the optimum temperature for viral growth is 33° C to 35° C.
Infections occur mainly in infants and children

Severe Acute Respiratory Syndrome (SARS) – CORONAVIRUS
Animal virus that adapted to and
became readily transmissible to humans.
Infection of lower respiratory tract
Fever, malaise, lymphopenia
High viral load
20-30% of patients infected with SARS require IC care; 10% mortality rate

Family Orthomyxoviridae

Influenza A, B, C

Influenza Type A and Type B viruses
Enveloped with hemagglutinin (H or HA) and neuraminidase (N or NA) glycoprotein spike proteins
HA= viral attachment protein
NA= facilitates the release of virus from infected cells

Influenza Type A and Type B viruses
The genomes: 8 single-stranded RNA segments,
 – The segmented genome promotes genetic diversity caused by mutation and reassortment of segments on infection with two different strains.

Antigenic Drift
Responsible for year to year variation in flu outbreaks
Influenza A has greatest rate of change
Minor variations- ongoing mutation with RNA encoding HA and NA proteins
Decreased immune recognition

Antigenic Shift
Major antigenic variations
Reassortment of circulating human strains with animal strains
Novel HA and/or NA = new viral subtype
Associated with pandemics and are restricted to influenza A viruses.
The principal reservoir for the antigenic shift variants of influenza virus appears to be animals, such as pigs, horses and fowl. They are likely sources of new antigens.
New virus has HA and/or NA that humans population has little/no immunity
Virus needs to be transmissible and replicate well in humans

Family Rhabdovirus
Ss RNA(-); bullet-shaped enveloped with G-proteins
Helical nucleocapsid
Zoonosis- wild animals and unvaccinated dogs and cats, bats


Source of virus:
Major: saliva in bite of rabid animal.
Minor: aerosols in bat caves containing rabid bats.
Risk populations
Veterinarians and animal handlers.
Person bitten by a rabid animal.
Inhabitants of countries with no pet vaccination program

Transmitted in saliva
 – also, transplanted infected tissues (e.g., cornea)
Virus replication
 – binds to nicotinic acetylcholine receptors on nerve endings & muscle cells
 – can remain at this stage for days-months; depends on how far away infection site is away from the brain

Retrograde travel to dorsal root ganglia and spinal cord
 – rapid ascent in spinal cord
Rapid infection of brain
 – neurons degenerate
 – little histopathologic change except Negri bodies; but this is variable
Afferent neurons take virus back to highly innervated sites

C. Perfringes
Alpha toxin

C. Difficile
Cytotoxin B

Sperical, enveloped, positive-strand ribonucleic acid (RNA) viruses

HIV virion
Two copies of ss (+) RNA
Consists of 3 major (Gag, Pol, Env) and 6 accessory genes
Two tRNAs (primers)
RNA-dependent DNA polymerase (reverse transcriptase)
Envelope- viral glycoproteins

Viral Core proteins:
Capsid- p24



GAG and POL are cut by
Protease – which is what is targeted by HIV drugs

Primary HIV Infection Syndrome
Occurs in 40-90% of patients: fever, malaise, myalgia,
lymphadenopathy, macular rash lasting from a few
days to several weeks. (Prompts 50% of patients to
seek medical attention.) Resolves with immune response to HIV.

Latent Phase
Most patients then enter an asymptomatic or
“latent” phase that can last from several months to
>15 yrs. HIV replication levels off and CD4 #s slowly
decline, observe non-life threatening diseases related
to immunodeficiency.

“Full Blown AIDS”: CD4 T cell numbers drop to less
than 200 cells/ul (normal is about 1000 cells/ul),
virus levels climb, prone to life-threatening

Reverse Transcripitase inhibitors

study of invertebrate animals capable of causing disease in humans and other animals

thick-walled, resistant, and resting cell

active, feeding, multiplying stage of most protozoa

zygotic cysts


asexual reproductive stage of an apicomplexan parasite (sporozoite stage). Multiple fission in which the nucleus divides first, and then the cell divides into as many parts as there are nuclei

Intermediate host
the immature form of parasite

Definitive host
host the mature form of parasite

Helminths are worm-like parasites

Parasite Life Cycles
Trophozoite stage: active, feeding, multiplying stage
Cyst stage: have protective membrane or thickened wall; usually have more resistant walls than cysts that form in tissues
Asexual reproduction
Sexual reproduction- Gametogony


worm-like parasites
multicellular with complex reproductive systems and life cycles involving intermediate hosts and a definitive hosts
Tough acellular cuticle
Trematodes: Flukes
Cestodes: Tapeworms
Nematodes: Roundworms

Blood and Tissue Protozoa
Plasmodium, Toxoplasma gondi

Malaria Plasmodium species
2 hosts:
Mosquito (Anopheles) for sexual reproduction (gametogony)
Humans/ animals for asexual reproduction (schizogony)
4 species & diseases (cycles of paraxysms)
P. vivax (Benign tertian)
P. ovale (Benign tertian)
P. malariae (Quartan or malarial)
P. falciparum (Malignant tertian)

Plasmodium Life Cycle: Liver Stage
Sporozoites enter the circulatory system and invade a hepatocyte
Sporozoite surface circumsporoite protein (CSP) binds heparan sulfate proteoglycans (HSPGs) on hepatocytes
Undergo asexual replication
The progeny, called merozoites, are released into the circulatory system following rupture of the host hepatocyte

Dormant phase of P. vivax and P. ovale
Some sporozoites do not immediately undergo asexual replication
Can reactivate and undergo schizogony at a later time = RELAPSE

is used to describe the situation in which parasitemia falls below detectable levels and then later increases to a patent parasitemia

Erythrocytic Cycle
Merozoites enter the RBC after being released from hepatocytes
Asexual replication progresses through a series of stages (ring, trophozoite, schizont) that culminates in the rupture of the erythrocyte

Malaria: Plasmodium: Clinical Disease
chronic disease
Paroxysms- typical pattern of chills, fever, and malarial rigors
reappear periodically
severity of the attack depends on the Plasmodium species as well as general health of host
Usually last 4-8 hours
Sudden onset of chills (Cold stage) and vigorous shivering; patient has fever
Hot stage- the patient feels an intense heat accompanied by severe headache, fatigue, dizziness, anorexia, myalgia
Profuse sweating will ensue and the fever will start to decline.
The patient is exhausted and weak
Does not exhibit symptoms until the onset of the next paroxysm.

Toxoplasma gondii

Definitive host- cat and other feline
Essential reservoir
Host that parasite passes its adult and sexual existence
Intermediate hosts- poultry, rodents, cattle, etc
Host that parasite passes its larval or nonsexual existence

Toxoplasma gondi: Epidemiology & Transmission
Ingestion of undercooked meat or other food contaminated with cysts
Contact with cat feces
Worldwide zoonosis
20- 40 % of the US population is seropositive
In Europe, as much as 90% are seropositive
Habits of eating raw or undercooked meat

Intestinal Protozoa
Entamoeba histolytica,
Giardia lamblia

Entamoeba histolytica
Life Cycle
Ingestion of cysts
Gastric acid in stomach stimulates release of trophozoite
Trophozoite released in duodenum
Trophozoite divide (binary fission) and cause pathology in large intestine.
Extraintestinal amebiasis can occur from invasion of trophozoite into deeper mucosa and into circulation
Trophozoite and cysts are passed in feces and are diagnostic of infection

Giardia lamblia (G. duodenalis, G. intestinalis)
AKA: G. duodenalis, G. intestinalis
Cyst and trophozoite forms
“Falling leaf” motility
Trophozoite absorbs nutrients from the intestinal lumen via pinocytosis

Giardia lamblia: Epidemiology & Transmission
Fecal-oral route
Contaminated water, uncooked vegetables and fruits
Oral-anal route
Risk factors
Poor sanitary conditions
Travel to know endemic regions
Campers, Hikers
Consumption of inadequately treated water
Daycare centers

Giardia lamblia
Life cycle
Ingestion of cysts
Gastric acid of stomach stimulates excystation
Release of trophozoites in duodenum and jejunum
Trophozoites replicate by binary fission
Use ventral sucking disk to attach to intestinal villi
Trophozoites and cysts passed in feces

Giardia lamblia: Pathogenesis

Ventral sucking disks attach to lining of duodenal wall, causing a fatty, foul-smelling diarrhea
Flattened intestinal villi and inflammation of intestinal mucosa with hyperplasia and lymphoid follicles
There is not a high degree of tissue necrosis

Helminths types
Trematodes: Fluke
Cestodes: Tapeworm
Nematodes: Roundworm
Enterobius vermicularis
Ascaris lumbricoides

Schistosomiasis: Schistosoma mansoni, S. japonicum, and S. haematobium
Second most prevalent tropical disease in the world
Endemic regions are where there is fresh water with the appropriate type of snail intermediate host
not endemic to the United States
Transmission is via skin penetration 

In water, eggs hatch into miracidia, which penetrate snail intermediate hosts
Maturation into cercariae occurs in snail
Infective cercariae swim, penetrate the skin of the human host

Schistosomiasis three types
S haematobium: venous plexus near the urinary bladder and ureters
S mansoni: inferior mesenteric vein
S japonicum: superior mesenteric vein of both the large and small intestines
Females deposit eggs in small venules
Eggs move toward lumen of intestine and of bladder and ureters
They are eliminated in feces or urine.

Schistosomiasis clinical manifestations
Heavy infection can cause symptoms such as cough and fever.

Nematodes/ Roundworms
Unsegmented bodies
Live primarily as adult worms in the intestinal tract
Diagnostics usually includes detecting eggs in feces

Enterobius vermicularis
Small, white worm
Worms live free in the intestinal lumen
Most common helminthic infection in North America.
Fecal-oral transmission
Infestation often occurs in family clusters

Enterobius vermicularis: Clinical Manifestations
Most are asymptomatic.
Anal itching (pruritus) or a prickling sensation , usually nocturnal or in the early morning.
a gravid female pinworm migrates to the anal area and inserts her tail pin into the mucosa for ovideposition.
Abdominal pain, Irritability, Restlessness, Vaginal itching, Pelvic pain
Re-infection is common, especially if not all contacts are treated simultaneously

Ascaris lumbricoides
Largest of the intestinal nematodes affecting humans, measuring 15-35 cm in length in adulthood
Most common helminthic infection worldwide
Prevalent in areas where sanitation is poor

Heterotrophic- dependent on complex organic substances for nutrition
rigid cell wall composed of chitin, glucan, and mannan
cell membrane in which ergosterol is substituted for cholesterol as the major sterol component

Fungi Morphology
Multicellular and comprise filamentous structures
Ability to transform between both a yeast form and a mold form in response to specific changes in environment

Unicellular, round or oval
Budding or by fission (asexual)
Bud is called blastoconidia
The daughter cells may elongate to form sausage-like pseudohyphae
produce round, pasty, or mucoid colonies on agar

Multicellular, grow in hyphal forms
threadlike tubular structures called hyphae, collectively called mycelium.
Septate- divided by partitions or cross walls perpendicular to the length of hyphae
Non-septate or coenocytic- multinucleate without cross walls
Fuzzy outgrowth or mold grows above the surface of agar
Aerial hyphae
Part of mycelium grows into agar for nutrients

KOH Preparation for fungi
The potassium hydroxide (10%) lyses or destroys most cellular material /debris and allows the fungus or components to be more easily seen.

Sabouraud’s agar

A culture medium for fungi containing neopeptone or polypeptone agar and glucose, with final ~pH 5.0-5.6

Cutaneous Mycoses

Dermatophyte Genera- filamentous (monomorphic)
The various forms of dermatophytosis are referred to as “tineas” or ringworm

Tinea cruris

Jock itch
Infection of the groin, perianal, and perineal areas, and occasionally the upper thighs
Trichophyton and Epidermophytom
Lesions are erythematous to brown and covered with thin, dry scales Tinea cruris

Tinea pedis
Athlete’s foot

The feet, especially the soles and toe webs, are most frequently involved
Trichophyton and Epidermophytom

Dermatophyte: Diagnosis

KOH preparation of skin or nail scrapings
Hyphae and arthroconidia
calcofluor white

Blastomyces dermatitidis: Morphology

Yeasts at 37C
Buds attached to the parent cell by broad bases
thick cell wall of the yeasts provides resistance to phagocytosis
Hyphae and conidia at 25C

Blastomyces dermatitidis: Clinical

Skin involvement; often without evident pulmonary lesions or systemic symptoms.
more common- face, neck, and extremities
Start as sharply demarcated papule and expand to form ulcerated lesions with small pustules at the margins.
Can become chronic
CNS involvement
Tends to be associated with patients who are immunocompromised

Oropharyngeal candidiasis

Symptoms may be absent or include burning or dryness of the mouth, loss of taste, and pain on swallowing
white plaques that resemble milk curd form on the buccal mucosa and less commonly on the tongue, gums, the palate or the pharynx.
Not commonly seen in healthy adults, but can present infants and elderly

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